


Upheaval

by Veralidaine



Category: Star Trek: Alternate Original Series (Movies)
Genre: Alpha/Beta/Omega Dynamics, Alpha/Omega, Khan's blood does funky things to Jim's anatomy, M/M, Miscarriage, Mpreg
Language: English
Status: In-Progress
Published: 2013-07-19
Updated: 2014-11-17
Packaged: 2017-12-20 16:13:31
Rating: Mature
Warnings: Creator Chose Not To Use Archive Warnings
Chapters: 8
Words: 12,920
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/889270
Author URL: https://archiveofourown.org/users/Veralidaine/pseuds/Veralidaine
Summary: <blockquote class="userstuff">
              <p>A fill for a prompt at the kink meme.  When Khan's people were created, their genetic modifications had the side effect of creating new genders; alpha,beta, and omega.</p><p>When his blood is used to revive Kirk, Jim's body is changed to complement Khan's, who is an alpha.</p>
            </blockquote>





	1. Chapter 1

**Author's Note:**

> Okay, I'm still working on this but I thought I'd start transferring it over to AO3 to make it a little easier to read.

Khan drifted in and out of oblivion on the biobed next to James Kirk’s. He knew that he was being kept heavily tranquilised and he knew his blood was being used to revive the captain. The latent scientist in him was intrigued by the prospect of observing what effect his blood had on the man—he hadn’t stuck around to find out what happened to the girl—but before he could give it more thought he was sent back under.

The augmented human was next awakened by a smell and a commotion. The smell was something he didn’t think he’d ever sense again, and the commotion seemed to be centred around the captain’s bed, also the origin of the smell. Turning his head and opening his eyes slightly, he could just see the curled up position and the shaking of the bed’s occupant. He heard the gruff voice of the doctor say something about strange brain activity and his eyes widened as his frankly superior intellect processed the most likely effect that his blood had on Kirk. Unfortunately in that moment, the doctor looked up and their eyes met.

“So you’re awake, then.” The gruff voice huffed sounding none too pleased. Khan raised an eyebrow and nodded.

“I believe that Mr. Kirk is in need of my assistance.”

“That’s Captain to you, and no, he no longer needs any of your assistance thank you very much.” The man looked at a nurse that was standing at the foot of Kirk’s bed. “Put him back under,” he ordered. The nurse nodded and stepped over to Khan’s IV drip. He was plunged back into oblivion and the next time he awoke, he was back in the brig.

When James Kirk awoke, it was to a stabbing pain in his abdomen. He scrunched his eyes and tried to breathe through it only to have another follow in its wake. Clearly, this was significantly affecting his heart rate because the doors to the biobeds opened and Bones, along with two nurses, rushed to Jim’s side. “You can’t just heal normally, can you?” McCoy grumped as he held his scanner over the captain. 

Jim smiled slightly in spite of himself, “Nice to see you too, Bones.” He finished with a groan as another spasm swept through him. 

McCoy cursed, “This doggone scanner isn’t giving me anything. For all I know, this could just be your vital organs starting back up.”

Kirk quirked his eyebrow at his friend before shuddering through more abdominal pain. Once he could speak again, he asked slightly sarcastically, “About that...care to explain to me how exactly I’m still alive? I mean, I know you’re good but not that good.” He curled around himself as another cramp hit him. 

The older man snorted, “You’re lucky I won’t kick a dog when it’s down, kid. Normally, that comment would’ve cost you.”

“Did you just call me a dog, Bones?” was asked in an incredulous tone as Jim looked at his friend with feigned shock. It wasn’t long before his eyelids shut again and a groan sounded. 

McCoy sighed, “We gave you Khan’s blood.” He said bluntly. Shocked blue eyes stared up at him.

“You did what? Ewwww.” The doctor rolled his eyes.

“It was the only thing that could revive you. I had done some tests on it already, and its ability to restore cells is unparalleled.”

“Please tell me you did tests on something living before injecting me with that shit.” 

McCoy scowled, “Of course I did. Dammit man, I’m a doctor, not a wet behind the ears ensign.” That got him another smile, which the gruff doctor wouldn’t admit gave him a warm feeling. He continued, “I injected a recently deceased tribble with some of Khan’s blood and lo and behold, the furball started moving again. Now, it didn’t seem to have any problems like this but I suppose there’s only so much that can be observed in a walking ball of fluff.” His patient let out a pained chuckle and McCoy came to a decision, taking a syringe out of his pocket and stepping over to Kirk’s IV drip. “Okay kid, I’m hesitant to do much else because I don’t want to interfere with any good work that blood’s doing on your system but I can give you a light sedative so you’ll sleep through the rest of the pain.” The blonde was barely able to nod his acquiescence before he was fast asleep.

McCoy looked over to the nurse on duty, “keep a nervous system scan on him and if there’s anything but rhythmic contractions occurring, comm me.” Not stopping to see her nod, the doctor made his way to the brig. It was empty except for one man, who turned slowly to face the newcomer.

“Ah, Doctor, I was wondering when you would seek me out.”

“Oh, cut the all-knowing crap, Khan, and just tell me what the hell is happening to Jim.”

“The captain is experiencing a few changes in addition to being alive when he had previously been dead,” was the enigmatic answer. The augmented human only smirked when he heard the other mutter something that sounded suspiciously like, “Son of a bitch.”

“So are you going to tell me anything useful?” Khan let out a long-suffering sigh.

“I’m afraid that any information I may have is for the captain’s ears alone.” The doctor’s hands fisted and he looked like he sorely wanted to cross the barrier to harm Khan but instead; the man simply turned around and swept out of the room. Khan smirked; he was going to enjoy this very much.

It was the next day when Jim marched into the brig, Bones and Spock on his heels. “Captain, I do not think it is wis-”

“Dammit man, I just finished putting you back together!” Jim stopped with his nose an inch from the glass and Khan met his stare full on.  
“I want to know what happened to me and I want to know it now!” A rumbling chuckle came from Khan’s chest.

“A bit impatient aren’t we?” When the blonde simply continued glaring, the superhuman’s eyes flickered first to the doctor, then to the half-vulcan. Kirk finally turned away and looked at his senior officers, nodding.

“I strongly suggest you reconsider your decision, captain--” Recognising the stubborn expression on his friend’s face, McCoy sighs and tells Spock to leave it and go back to the bridge. Whereas the first officer may have objected before, his newfound trust in the captain leads him to depart with only a penetrating stare at the prisoner.

Once his two friends had departed the brig, Jim turned his stare back on the occupant of the glass cell in front of him. “It is good to see you alive and well, Captain,” Khan says with a slightly sardonic smile.

“So, debilitating abdominal pain is just a normal side effect, then?” Kirk questioned dryly.

“Oh no Captain,” Khan stated silkily, “that would be your organs realigning.” He took a special satisfaction from the way the captain’s eyes bugged out.

“What?”

“Yes, your body is preparing itself to carry a child.” Kirk stared at the augmented human for a few more seconds before laughing bitterly, 

“You have a very warped sense of humour, Khan.” The man in question just smirked.

“You’ll find out soon enough.”

“Aaand with that vague, uninformative conversation under my belt, I’m returning to the bridge to oversee the numerous repairs needed to fix the damage you did to my ship.” Khan only continued smirking as Kirk left the brig.

After a shift on the bridge with no complications, Jim decided to listen to the niggling voice in the back of his head and visit sickbay before returning to his quarters. Luckily, McCoy didn’t seem too busy or Jim would have felt bad for taking up his friend’s time with what could potentially be nothing. As it was, he hopped up on a biobed and faced his friend’s quirked eyebrow. “Anything I can do for you Captain?” Jim smiled,

“Yeah Bones, could you do a scan of my stomach?” Leonard was surprised by the question but picked up his scanner. It was not every day that the captain allowed him to check that everything was working properly.

“Alright, anywhere in particular?”

“Yeah, a full body scan of anything between my collar bone and my pelvic bone.” The machine let out a slight whirring noise.

“Okay, the scan should be ready to view in 30 seconds.” Although the doctor tried to hide it, he couldn’t hold in a small yawn. Concerned for his friend and knowing that he probably had a pretty hectic couple days, what with Jim’s death and subsequent revival, the blonde placed his hand on the doctor’s arm.

“You know what, Bones? Why don’t you get some sleep? I need some too and I figure this is probably something that can wait until tomorrow.” He laughed at the irritated expression he was faced with.

“Well, why on earth did you need it done now if it’s so unimportant?” McCoy sniped. Jim gave an innocent smile and shrugged, hopping off the biobed and heading to the doors.

“Bye Bones,” he called cheerily before leaving to the sound of grumbling. McCoy decided to listen to his friend and placed the scanner on his office desk, resolving to look at it first thing in the morning. 

It was when the door to his quarters had shut when Jim realised that he was sweating. He tried to remember if the rest of the ship had felt like this or not and shrugged when he couldn’t. “Computer, please lower temperature by three degrees in this room.”

“Yes Captain, lowering temperature,” the mechanical voice stated. Frowning when he did not get the relief he wanted, Jim requested the temperature be lowered another two degrees. Once he was comfortable, he went into the bathroom to get ready for bed. As he walked out, he was surprised to hear the door buzz.

“Come,” he announced. The door slid open to reveal Spock, who stepped inside and was about to say something when he suddenly stilled, his brow crinkling the only sign that he was perplexed. “Is there something wrong, Spock?”

“Captain, I calculate that the temperature in your quarters is approximately five degrees below what most humans deem comfortable.” Jim shrugged,

“I was feeling a bit overheated when I got in.”

“Are you certain you are not ill? Perhaps it would be best to visit doctor McCoy.” The human chuckled,

“Spock, I’m sure it’s nothing but if it makes you feel any better, I’m visiting sickbay tomorrow morning so I’ll bring it up with Bones. Now, is there a reason you came to my quarters?”

“Yes Captain, I came to ascertain whether you would like to submit the report of what happened and inform Starfleet of Khan’s capture.”

“That sounds fine, Mr. Spock. I can leave it to you then?”

“Indeed, Captain.” Spock had turned to exit the captain’s quarters when Jim called his name.

“Thank you for worrying about me, Spock.” The first officer was about to inform his captain that Vulcans did not feel worry but stopped himself and simply nodded before leaving. Jim smiled to himself before undressing and slipping under his covers. Just as he is about to drift off, he feels a slight dampness around his behind but the thought doesn’t get a chance to take hold before Kirk is fast asleep.


	2. Chapter 2

The next morning, Jim was surprised to wake up from the best wet dream he’d had in a long time. He wasn’t surprised that he had one--it’s a rare night that he doesn’t have wet dreams—but rather, he was surprised because he had been penetrated and enjoyed it. Now, Jim wasn’t new to encounters with men—he’d definitely been around that block a few times—but he was always the one doing the penetrating. This dream featured a tall, well-muscled featureless man pounding into him and Jim couldn’t remember the last time he had wanted so badly. As he got up to pick up his comm, which had woken him with its buzzing, he absently noted that there was an awful lot of fluid on his sheets but chalked it up to being well-hydrated. As soon as he answered his comm, he was being told by Bones to come down to sickbay because he ‘really needed to take a look at something.’

McCoy had seen a lot of things during his medical career but this was certainly one of the rarer ones; he was speechless as he handed over the scans of Jim’s torso and abdomen. “Uh...Bones? I’m not quite sure what I’m looking at but I’m pretty sure it’s not supposed to look like this.” Instead of making a snide comment, McCoy decided to just explain the changes to Kirk as directly as possible.

He pointed at various parts of the scan, “That’s your rib cage, those are your lungs, that’s your stomach, that’s your liver, those are your ovaries, and that’s your uterus.” The captain seemed to choke on his own spit for a moment before turning and staring at his friend, blue eyes like dinner plates. He then promptly fell unconscious. McCoy rolled his eyes, “Figures. The kid can stay conscious during debilitating neuromuscular pain but tell him he has functioning lady parts and wham!” He called over to a nurse and together they manoeuvred the captain onto a biobed before both departed for other patients.

Khan wasn’t surprised that afternoon to see a furious James Kirk heading towards his cell; it was only a matter of time. Again, the man stopped with his nose an inch from the glass before brusquely asking, “So, are there any other side effects I should know about?”

“Right to the point, I see. I suppose you have started feeling overheated?” Jim looked momentarily surprised before nodding; he hadn’t realised that was related to this. The brunette waved his hand dismissively, “Normal.” Kirk narrowed his eyes at the prisoner’s relaxed, nonchalant attitude before whispering furiously, “And I guess it’s also normal to leak fluid from my anus?” Khan smirked,

“For an omega in heat, it is. Of course, you won’t always be in heat.” The captain’s eyebrows raised.

“An omega,” he repeated, curious.

“That is what you are now that my blood has changed your organs and brain chemistry.” Khan’s smirk widened as he watched the blonde start to squirm in his stance. Perhaps his presence was having an accelerating effect on the new omega’s heat. He eyed the expandable window that had previously allowed the doctor to take his blood, and lowered his voice to a rumbling purr. “Let me stick my arm through.” Although there was a slight glaze in Kirk’s eyes from the change in tone, a voice in the back of his head made him narrow his eyes and look at the augmented human suspiciously.  
“Why should I do that?” Khan sighed in a put upon way,

“because it will be much more informative than any medical scans.” The blonde continued to glare at the other but pulled the window towards him and enlarged it so that an adult arm could fit through comfortably. Khan took a moment to judge the smell coming through the hole before placing his arm through it and reaching his hand towards the young captain. Jim instinctively stepped back but Khan knew he had his attention when Jim’s nostrils flared. The new omega stepped forward and gripped the exposed forearm, bringing the wrist to his nose. His eyes closed in pleasure as he took deep inhales of the scent Khan knew was being secreted by two glands on his wrist. When a pink tongue swiped across the brunette’s pulse point, he pulled his arm back into the cell, but not before shuddering at the warm, wet contact. The new omega let loose an endearing whimper and tried to follow the progress of the arm before blinking and seeming to partly come back to himself. 

Khan decided to take pity on the captain, who now looked disgusted with himself, and explain. “I am what my people call an Alpha, the perfect match to your Omega,” the deep voice rumbled, “although I had known that my blood had healing properties, I had not realised that it might alter the brain chemistry of an ordinary human, such as you were. I can’t say I’m displeased with the results.” Nodding at the window, Khan continued, “Why don’t you open that window a little larger, Captain? I think we have already established that I do not wish to harm you.” Still dazed from the earlier scenting, Jim followed the suggestion, expanding the window so that a man could fit his shoulders through. 

Quickly, so that the flighty omega wouldn’t have time to pull back, the augmented human stuck his torso through the hole and drew Kirk into a searing kiss. Normally, Jim was the one to dominate any sexual encounters he had but this time his instincts told him to submit so he did, relaxing his mouth and letting the alpha drive the kiss forward. When they parted, Jim was so shaken from his loss of control that he shoved the alpha back into the cell and shrunk the hole before flinging it to the side. Khan swore; if he hadn’t been thrown off by how much he enjoyed the kiss, he could have anticipated the captain’s actions and resisted but as it was, he had to watch as his omega strode away looking disturbed.

“Why run, Captain? It’s clear that we are good together,” he called, “you know that I’m the only one who can give you what you need.” The brig doors slid shut behind Kirk and Khan sat on his bare cot, determined to wait for what he deemed inevitable.

Jim stumbled into his quarters, eyes wide as he tried to process what just happened. He could still smell Khan’s potent scent and the taste that he had gotten, both from Khan’s wrist and from the kiss, was still on his tongue. It had been tortuous to leave that cell and now all he could think about was going back. He sat down on his cot and put his head in his hands, he couldn’t let this shake him from what he was supposed to be doing. Khan was a prisoner that would be taken back to Earth by the Enterprise, and Kirk was that ship’s captain. 

Jim wondered whether he should look further into this Alpha/Omega business but dismissed the idea. There was no way he would risk Spock or Bones discovering his state. After all, it seemed like he would only be dealing with some discomfort until his ‘heat’ passed. Speaking of which, Jim had noticed that the back of his regulation pants were pretty wet. Heading into the bathroom, the blonde slipped his pants off and looked at them. Luckily, the colour and thickness of the material meant that there was only a slight visual change between the wet and dry parts. Anything short of a Vulcan probably wouldn’t notice it and Jim was relieved to note that he hadn’t passed any Vulcans or Half-Vulcans in the hallways earlier. 

Jim slipped off his underwear and placed them in the hamper with his pants. He then decided to get a better lock at the changes to his body, turning so his back was facing the bathroom mirror, pulling his bum cheeks apart, and looking over his shoulder. The crinkled skin around his butthole was red, reflecting the itchy-sore feeling that had been plaguing Kirk for the last day. Gingerly, Jim reached a finger to touch the puckered hole but found that with all the lubrication, the tip of his finger slid in without him trying. Almost immediately, the itchy-soreness dulled to a point where it was barely felt, and Jim was surprised at the amount of pleasure sprung up from that small amount of contact. He gave his finger an experimental wiggle and moaned at the sensations. After a few more wiggles, the blonde decided that he needed more and gently slid a second finger into his anal cavity. Due to how relaxed and lubricated he was, it went in without a problem, and boy did he reap the rewards. Unfortunately, this too proved not to be enough after a few seconds and the angle didn’t allow him to stick any more fingers in. Additionally, he realised that his explorations had caused a slight ‘problem’ to spring up in the front. 

After some thinking, Kirk walked over to his personal replicator and replicated a small tube of lubricant, and entered in some specifications that the ship replicators had never made before. After some whirring, the machine finally materialised a cylindrical piece of safe hard plastic with a flared base; Captain James T. Kirk had just replicated himself a butt plug. Eager to try out his new toy, Jim laid back on the cot and worked the object into his loose opening, ever cognizant of his straining erection that was begging to be touched. 

With each movement of the piece, the blonde couldn’t hold back a groan of appreciation but it was when the smooth side brushed against a part of his inner wall, that Kirk really saw stars. He jerked slightly at the sudden shock of pleasure, his rigid member bobbing against his stomach. Once he had situated the plug comfortably in his anus, so that it was only lightly touching that amazing spot inside of him, he opened the tube of lubricant, squirted some on his hand, and gripped his erection. As he slid his hand up and down his penis, the slight movement caused the toy to brush his sweet spot repeatedly, slowly heightening his pleasure level. He sped up his movements, adding some twists of the hand closer to the head until finally his orgasm ripped through him. He was so happy to have some relief from the constant itchy ache that he now associated with ‘heat’ that he fell right to sleep.


	3. Chapter 3

When Jim woke up the next morning after yet more wet dreams, the first thing he noticed was how heart-wrenchingly empty his chest felt. The second thing he noticed was the renewed itchy ache in his butt but a simple clench was all it took to solve that mystery; his plug had fallen out. Gasping around the emotional pain, the blonde reached behind and worked the plug back into his still-relaxed hole, only to let out a sob when he realised that it only had a fraction of the dulling effect on the discomfort as before. Giving that up as a lost cause, Jim untangled the sweat-soaked sheets from his torso and looked down; nothing. There was absolutely nothing that suggested why he felt like he was on the verge of an emotional breakdown. It was only when he paused to take a deep breath that he realised what he was missing. Khan’s scent was no longer in his nose; it had faded with time. The captain didn’t want to think he was dependant on the prisoner’s smell but it was the only thing that made sense; the lack of the smell was the only factor that accompanied the horrible empty feeling.

Khan looked up to see the captain—his omega—enter the brig and swiftly make his way to the only occupied cell. Upon reaching the glass, the blonde moved the window into the centre and expanded it so that an arm could fit through. Wide blue eyes looked beseechingly at the alpha, “Please.” Kirk cut himself off, hating that he was reduced to begging. All of Khan’s instincts screamed at him to go and comfort his omega, who was so obviously in pain, but he held back.

“No,” the denial echoed sharply in the room. Before Kirk could say anything, the superhuman continued, “a sniff of my wrist isn’t going to help this time, Captain. If you want to avoid experiencing even more discomfort than you already are, you’re going to have to enter. It’s time that you fully accept what you are now, an omega that has needs only I can fulfill.” A shiver ran through the blonde and he bit his bottom lip, conflicted. Khan stayed silent, knowing that Kirk had to make this decision completely on his own. Finally, the young captain tapped something into the console next to the cell and stepped through the door that formed. It closed behind him and he stood there uncertainly,

“please make it stop,” he half-whimpered. Khan took a deep inhale of the now-potent pheromones and surrendered himself to his instincts, rushing forward and pulling the younger man into his arms. With his arms solidly around his omega and the blonde’s nose snuffling into his neck, the augmented human decided he would not be separated from his soon-to-be bondmate. He hoped that Kirk wouldn’t react too badly to finding himself tied to his once-nemesis and most likely pregnant but he had no desire to inform the new omega of these little bits of information to do with the Alpha/Omega relationships.

Khan slipped his hand down to cup Jim’s butt only to encounter something odd with his hand. Curious, he slipped the regulation pants down, and a wicked smirk alighted on his face. Kirk was too immersed in his alpha’s wonderful scent to register the sensation of his pants being pulled down, but he did feel the spark of pleasure shoot through him as the handle of the plug was jostled. He craned his neck up and saw the pleased expression on the brunette’s face. “I suppose you have been using this alleviate your discomfort?” Jim nodded meekly, as overtaken by his new instincts to submit and please as Khan was, by the instincts to care for and protect. “And did it help?” the alpha questioned.

“It did at first but then...”

“But then your body realised that no amount of molded plastic would ever replace a nice hard cock, hmm?” Jim groaned at the thought even as he shuddered at the dark, husky tone Khan’s voice had taken on.

The alpha eased the plug out, relishing Kirk’s moan as he did so. “So responsive,” he murmured, “I’m going to make you feel so much better than this thing ever did.” Jim keened and was pliant as Khan picked him up and placed him on all fours on the cot. Wasting no time, he placed the head of his already erect cock at his omega’s stretched opening and started pushing in. While the sphincter opened easily, Jim let out a distressed whimper as he realised that what was entering him now was much bigger than the plug had been. That noise was almost like a slap to Khan, and the now instinct-driven alpha stilled, allowing the blonde to get used to the new intrusion, before pushing forward again until thighs touched the captain’s well-rounded cheeks.

Khan allowed Jim a few seconds to again, acclimatise to the new fullness, before pulling out and thrusting back in. The blonde let out a little puff of air that contributed even more to making the augmented human want to protect this precious creature. It wasn’t long until the repeated thrusts were eliciting moans, and then shouts. As the brunette felt himself nearing his peak, he coated his right hand in some of the excess slick being expelled around the base of his penis and started stroking his omega’s shaft. He felt the base of his cock swell and forced it past the ring of muscle before his release hit him. As he deposited fertile seed into the even more fertile body before him, Khan tugged at his partner’s genitals until he felt the body shudder and his hand get splattered by liquid. A warm feeling filled the alpha’s chest at the thought of bringing his new mate pleasure and he manoeuvred them both onto their sides, his penis still stuck inside the omega.

Once Jim came down from the orgasm, he was horrified at his own behaviour. He tried to move forward, away from the body behind him but found that the movement sparked a pain in his rear end. He specifically tugged his groin forward and started to panic when it wouldn’t separate from Khan’s. A hand stilled his hip, “I’m afraid we will be held together for at least ten more minutes, Captain.”

“What? Why?” Jim’s heart was still beating wildily; he didn’t like feeling trapped.

“It is my knot, every alpha has one at the base of their penis. It is to ensure that the pair has time to bond.” He conveniently didn’t mention that it was also to give his sperm a maximal chance at impregnating the omega’s egg; no need to inform Kirk of that just yet.

The blonde was silent for a moment before snorting, “fat chance of that!” Khan hummed before nosing at Kirk’s hairline, relishing the shiver it elicited.  
“I think you’ll find, Captain, that your heat has only temporarily receded and will soon be back; most likely right after we separate ourselves.” Jim didn’t say anything after that and the brunette took the remaining moments of their bondage to imprint the smell of his mate in his brain.

Jim dozed for about ten minutes before feeling the now flaccid organ slip out of his rectum. Sure enough, a wave of warm-itchy-ache followed, starting in his stretched sphincter and radiating outward until his whole body was sweating and shaking slightly. It was the loud panting that alerted the man behind him, who immediately placed his wrist in front of the omega’s nose to provide some relief. Jim inhaled like a man deprived of oxygen, desperate to soothe what he was sure was a worse sensation than before. Although it subsided a little, Kirk still let out a little whimper, which spurred on his alpha, who was determined to provide for his new omega. 

Khan didn’t have to worry about his penis—it was already fully erect and straining due to the pheromones in the air—and was able to slip it back into the other man with little resistance. He built up a steady rhythm and relished the little keens and cries he was eliciting. Perhaps Jim was fully into his heat headspace now, for he appeared to be exposing the back of his neck to Khan. The brunette took full advantage of this and bit down as his knot swelled in the warm heat, drawing blood as his seed pumped into his omega’s reproductive organs. At first, Kirk cried out but he soon quieted and went boneless when the alpha started licking broad strokes along the bite mark. Noticing that one part of his omega’s body was certainly not boneless, Khan wrapped his hand around Jim’s organ, and started stroking, spreading the precum that he found at the head, as he went along. The blonde gasped, spurted, and went limp; the heat was really taking a lot out of him.  
The brunette’s eyes were drawn back to the bite mark and a small tear slid down his cheek at the warmth that encompassed his whole being. When he had first been woken from his cryotube, he had found himself surrounded by beings that did not have dynamics, and could not be certain that he would ever be able to wake the rest of his crew, although he knew he was going to try. He had basically given up on the idea of ever having an omega of his own, yet here he was, about to build a family with a beautiful omega that he knew he would love and cherish with an undying loyalty. He didn’t care that it was a former foe; that didn’t matter. After all, he and the captain were fairly similar; both passionate men who were intensely loyal to those he cared about. The alpha winced slightly at the knowledge that he would most likely have to tolerate the likes of the half-vulcan and the gruff doctor; they were Jim’s family after all and Khan couldn’t see himself denying his omega the right to see his family.

A pang went through the superhuman at the indirect thought of his lost family, but he pushed the pain aside as his omega stirred. Right in front of him was his family now, and this time there was no way he was losing it.


	4. Chapter 4

When Jim woke up this time, he felt the now-familiar need in his anal cavity that was clenching on empty air. It was not quite powerful enough to keep him from remembering the past events though. Wide-eyed, he reached his hand back to explore the bite mark on the back of his neck. His fingertips had just brushed the newly scarred tissue when his wrist was caught in a gentle grip and lifted away from the skin. “That is mine, and mine alone to touch,” rumbled from behind him. Jim blinked in surprise but pulled his hand away.

“Wha-what is it?” Not liking how shaky he sounded, he tried to summon the Kirk confidence. “I’ve had love bites before but this is a little excessive,” his chuckle fell flat.

“That is because this is a bond bite. It ties me to you and you to me.” Jim scrambled up into a standing position a few feet away so quickly that Khan coud only stand and face the panicked omega.

“What do you mean, ‘bond’? I didn’t ask for that!” Sparks jumped in the blonde’s eyes as he got angrier; Khan was mesmerised.

“Nonetheless, it is there now, we are mates for life.” As he spoke, he slowly took a step forward.

“Don’t move!” Jim warned, “I’ll call Spock and Bones!”  
“Ah yes, the two sidekicks, I had wondered why they haven’t shown up yet.” Kirk narrowed his eyes at the name and muttered,

“I may have told them that I needed a few days to rest without being bothered.” The brunette smirked,

“then they can wait a little longer.” Before he could take another step, though, Jim had brushed the glass with his thumb and slipped through. The augment assumed that it was an emergency setting that recognised whoever pre-programmed it. He rushed it anyway and wasn’t surprised when he hit the glass, the impact barely registering on his superior body, although it made quite a loud noise. “You fool!” His baritone voice echoed around the brig, “it’s too early in the bonding process for us to be separated!” The captain on the Enterprise collapsed against the glass just as the brig doors slid open and two security officers rushed in, having heard the commotion.

“Captain!” One of the red shirts exclaimed as the other drew his phaser and pointed it at Khan, even though the superhuman was safely behind glass. Jim, overwhelmed by the sudden wave of pain that seemed to come out of nowhere, just managed to ask for Spock. One of the officers called for Spock and both the half-vulcan and the gruff doctor entered the brig not five minutes later. McCoy kneeled by his friend and took a reading with his tricorder. Spock reached down to help Jim up.

“Don’t touch him!” The deep voice snarled from the other side of the glass. Leonard startled, not having noticed anybody else but his suffering best friend but Spock simply looked up with cool brown eyes.

“And what reasoning is behind your demand, prisoner?”

“He is my mate!” The alpha was in an animalistic frenzy now, all bright eyes and gnashing teeth, but still managed to explain. “My blood changed him to be like me, the omega to my alpha. We are bonded but we were not to be separated for a day yet. He foolishly stepped out of this cell, sealing himself off from my scent.” McCoy’s head swung up from where he was trying to make sense of the readings.

“Alpha to your omega, eh?” He murmured thoughtfully. Spock looked down at him,

“Doctor, are you aware of this phenomenon?” Leonard looked up at the half-vulcan before looking back at Khan.

“It was mentioned briefly in an advanced xenobiology class. It’s a sort of...dynamic that exists in certain species.” Khan’s nostrils flared when the downed captain let out a whimper, curling more tightly around himself.

“Explanations can wait, Doctor, my omega needs me.”

“I do not believe that is an advisable acti--”

“No, he’s right Spock. If what we’re dealing with here is what was talked about in that class, then the worst thing for Jim is to keep him away from his alpha.”  
Bones reached over to the expandable window, pulled it closer to Jim, and expanded it. Khan immediately put his arm through so his wrist was in front of Jim’s face. The omega’s nostrils twitch before he grappled at the forearm, eventually pressing his nose against the skin. His entire countenance relaxed and McCoy did another scan only to find that the data that had been changing rapidly a moment ago was now stabilising. 

Upon seeing that his captain was no longer in pain, Spock murmured, “fascinating”. Although he did not trust Khan, it was evident to him that the prisoner’s presence was necessary for the maintained good health of his friend. This is why he did not object when the doctor opened up the window larger and pushed the captain into the cell and into the prisoner’s arms. As he and the doctor walked out of the brig and back towards the bridge, McCoy explained what had occurred, including connecting the dots between this and Jim’s new equipment.

Back in the cell Khan was looking down at his omega, who was sleeping off the effects of the separation happily ensconced in his alpha’s arms. He knew that the separation had probably pushed aside the heat and that the heat would come back three times as powerful once Jim’s body was back to normal. He would have to be extra alert in the coming hour; as much as he was unhappy with his omega for leaving the cell, he did not wish suffering on the blonde. No, he would provide for his omega, even if it means protecting Kirk from his own ignorance.

As Jim woke up, he idly wondered if he had fallen to sleep in a furnace and it wasn’t long before his body communicated to him that it was in severe discomfort. His remaining grogginess left him more submissive than usual and he leant back into the comforting presence. Khan was woken by a distressed mewl and it took him a few seconds to realise that it had come from his omega.

“You should not have left” he rumbled. The blonde captain stiffened, which caused the alpha to sigh. He supposed that he admired the stubbornness in his omega, even if it was inconvenient. Luckily, he now had a means of dealing with Kirk’s more rebellious moments, such as trying to leave Khan’s embrace, which is what the younger man was trying to do at the moment. The brunette leaned down and mouthed at the bond bite, which caused the omega’s body to melt against him. Jim panicked at his inability to move his muscles but could do nothing but hyperventilate. The superhuman swore at the sounds of the ragged breathing and placed his lips on the mark again, sucking on the skin. The breathing immediately slowed and Jim’s eyelids fell partly closed as he was rolled onto his back, but Khan could see his eyes flicking madly from side to side.

“What-what is this?” was the plaintive request.

"Those are the effects of the bond bite. When you are in heat, my saliva can elicit a relaxing response on your body depending on how long it is in contact with your skin. It is normally only used to soothe omegas that have very uncomfortable heats but occasionally it is needed to protect a recalcitrant omega from himself.” This was accompanied by a pointed glare and the blonde had the decency to look a little cowed. Knowing that now was not the time to be too hard on Kirk, the alpha slipped the shirt off the now pliant body and ran his hands down his mate’s chest, eliciting a shiver. “Now, shall we begin?” Now that Jim was again paying attention to the burning all over his body that seemed only doused by the other’s touch, he could do nothing but nod helplessly.

Khan moved himself so that he was staring at the leaking orifice through which he would be joining with his mate. He eased two fingers through the sphincter, making sure that the passage was still stretched enough to accommodate his organ without pain. As he re-stretched the area, he made sure to brush the omega’s prostrate to bring him some pleasure and relief. It wasn’t long before he was, once more, easing his penis into the loose passage. Jim panted, his eyes glazed with pleasure, as Khan--his alpha, a little voice in his head reminded him—thrust into him—staked his claim. Kirk had never felt so owned in his life, and yet it didn’t feel restrictive at all. In fact, it seemed to bring a whole new type of freedom; Jim no longer had to prove himself in everything he did, he now had somebody who would love him unconditionally. 

Oh, he was sure that Bones loved him—that’s why he saved his best grumping for Jim—and Spock probably felt a large amount of affection for him as well—he did cry when Jim was dying—but the blonde had to share that affection with others; Spock’s with Uhura, and Bones’ with his patients. Here was a being that could devote all his attention to the young captain. A small spark of fear alit in his chest upon thinking about Khan’s family, still safely in their cryotubes on the enterprise. Once they told the superhuman—and truthfully, it would be cruel not to—would Khan drop him like a sack of potatoes? This train of thought was brought to an abrupt halt when the alpha changed his angle and started pounding into what Jim knew to be his prostrate. Waves of pleasure drove him higher until he finally crested, mouth opening in a silent scream as Khan drove his inflated knot through the relaxed sphincter and followed with his own orgasm.  
Tears came to Jim’s eyes as he realised that even as the knot tied them together, the burning didn’t stop. In fact, as soon as pleasure was no longer hitting his nervous system, the discomfort appeared and grew. His growing whimpers soon caught the attention of his alpha who licked at the bond mark, eliciting a wave of cooling relief.

“I will do my best to reduce your discomfort but I hope that you will take this as proof that you should not run from me when in heat, my mate.” The blonde keened as Khan gave the mark another lick. The brunette moved a hand along the front of Kirk’s torso, feeling the quivering abdominal muscles and rib cage until he reached the omega’s left nipple, circling and teasing it with his thumb. This elicited a small gasp of pleasure. Khan decided to up the assault by nibbling and kissing at the side of Jim’s neck while continuing to tweak the now-hardened nubs. This caused the captain to lean his head back over the superhuman’s shoulder and arch his back, trying to get closer to the stimulation while not being able to move his lower half.

The alpha kept this up until his knot deflated and he was able to disengage, allowing him to flip Kirk onto his back, lean over him and latch his mouth onto his right nipple. Jim shouted out, fisting his hands in the augment’s hair before running them down the muscled shoulders and back. He keened at the power that he could feel in the coiled muscles; he had never felt so safe and protected. As soon as the wet heat left his sensitive nub, the blonde lightly tugged at his partner’s head, bringing their lips together in a searing kiss. He put all his feelings into it, unknowingly signalling his acceptance of this new dynamic. After a moment of surprise, Khan responded enthusiastically and took control of kiss, further rejoicing at his mate’s immediate submission.

His right hand slowly migrated south until it could feel the slick that was already leaking out of his poor omega’s inflamed hole. He teasingly rubbed his finger around the perineum but soon pushed it through the relaxed ring of muscle upon hearing Kirk’s moan of discomfort. The knowledge of the captain already being ready for him soon had Khan hard again and he wasted no time in lining up his organ and pushing home. This was the first time he was facing his mate as they joined and the augment delighted in the expressions he was now witness to. The blonde’s eyes repeatedly opened and closed as his prostate was hammered again and again.

After being knotted three more times, the blonde finally seemed to be sated and slipped into sleep. Khan almost collapsed next to his omega, unsure of whether he could have formed another knot if Kirk had wanted more. To his relief, he noted that the heat would most likely be finished when the pair woke up tomorrow. With that thought, the superhuman followed his mate into slumber.

**Notes for the Chapter:**

> So there's all that I have so far. Hopefully I'll have the next chapter up soon.


	5. Chapter 5

**Notes for the Chapter:**

> Blargh, sorry for taking so long. Real life decided to be really demanding. I hope you like this.

Khan was dismayed the next morning to find himself alone in his cell. In addition, it seemed that he had slept through a cleaning crew because he could not see any evidence of coupling, nor could he smell a hint of his omega’s sweet scent. As the augment pulled himself into a sitting position he tried to push away the encroaching hurt that he couldn’t help but feel in response to the perceived rejection. There wasn’t anything else he could do but wait for his mate to approach him again.

Meanwhile, on the bridge, Captain James T. Kirk was seated comfortably in his chair after having given his crew a heavily revised explanation of why he had been absent the last few days. He relished the hum of the machinery and wasn’t even discouraged when his yeoman dumped a large amount of PADDs requiring signatures into his lap. It was a couple days later when, after a harrowing away mission, Jim was forced to once again seek out the company of his alpha, whom he had most definitely not been having wet dreams about.

The away mission involved the captain and a group of male officers going down to a planet referred to as ‘Laxon’ for negotiations. It had been discovered that the socially behind planet regarded females as incapable when Uhura had tried to contact the planet’s leaders, only to be rebuffed. Jim figured that Spock would be calming his partner’s ruffled feathers for a while yet.

Once the group had beamed down into the centre of the main city, Jim had been about to approach the leader when the latter became enraged. He was convinced that he was being dishonoured by there being female in the group. Confused, Jim tried to explain that there was no female in their landing party when the leader yelled, “Silence, female!” 

Kirk fell silent in shock but Spock was quick to step forward and sternly reprimanded, “Sir, that is the captain you are referring to and he is a male. Please show him the proper respect.” The planet leader turned to look at the half-Vulcan.

“You say your captain is a male. Am I to take it, then, that the males of their species are the ones who carry the young?” Spock’s eyebrows furrow slightly, showing his confusion.

“No, I am quite certain only human females can carry young.”

“Then you are either mistaken or you take me for a fool. My kind are always aware of the state of fertility of beings and your captain is currently carrying young, thus proving that she is female.” The being then waved his hand dismissingly and turned away, now appearing bored with the proceedings. Silence followed his pronouncement. After a moment, Jim turned to his first officer.

“Spock, I can trust that you will carry through with these negotiations?” The half-Vulcan nodded, seemingly speechless, his eyes running up and down his friend’s body. Jim called Scotty on his comm and returned to his ship in a flurry of lights. He calmly walked through the halls to medbay and sat on one of the biobeds to wait for the Doctor to finish with his other patients. When Bones saw the blond, one of his eyebrows raised but he stayed silent upon seeing the grim expression.

“Can you do another scan of my stomach?”

“Another one? Didn’t we already establish that you had extra organs? I can’t just use expensive equipment to suit your every whim,” was the crabby response.

“Well, something might have changed,” was stated tiredly. McCoy’s hands stilled from where they had been fiddling with the scanner and his eyes narrowed.

“You didn’t use protection with Khan, did you? Dammit Jim!” He placed the scanner along Jim’s breastbone and with steady hands, drew it downwards. When he was finished, he put the equipment aside and looked at the Captain with a disapproving expression. “Well, we’ll find out for sure in under a minute.”

Once the scan was ready, Bones examined it before announcing, “congratulations kid! It’s a boy,” in a sardonic tone. There was a thunk as the blond once again passed out on the biobed. “Godammit!”

Khan lifted his head from his cot upon the feel of long-tense muscles relaxing. He did not need to look towards the glass to know that his mate had returned, but looking did tell him that judging by the surprised look on Jim’s face, he too felt something upon entering the brig. Without a word, the captain entered the cell and came forward to stand a couple feet in front of the cot. The augment moved his body into a sitting position but tamped down on the urge to rush over and embrace his omega. The two looked at each other for a few moments until Kirk shuffled forward a few steps. Again, the alpha had to exert effort to maintain his calm and relaxed demeanor as he knew that had to let the blond become comfortable with him though his own decisions and actions. Finally, Jim lowered himself gingerly onto the cot next to the brunette, shoulders hunched and gaze lowered in contemplation.

“We’re having a boy,” he announced into the silence, voice full of wonder and a long ago decided upon sense of resignation. Khan made a noise of acknowledgement which caused the Starfleet officer to look up at the other man. “You knew this was going to happen?” Although slightly accusatory, the superhuman was pleased to note that there was no real anger in the blond’s voice. Regardless of previous feelings about the man sitting beside him, Khan wanted things to go well with his mate.

“You were in heat. There is a 98.8% choice that an omega in heat will have conceived by the end of coitus.”   
Jim snorted, “Now you sound like Spock.” Although the alpha did not appreciate being compared to the half-vulcan, he was glad to see the display of good humour and decided to take advantage of it. Casually, he reached out and enclosed the captains’s right hand with his left. Aside from a slight stiffening, he was pleased to note that his omega did not pull away. He started stroking the skin between the thumb and forefinger with his thumb and soon felt the limb relax completely. Spurred on by this victory, Khan used his right hand to gently move the blond’s chin so that he was looking intently into the bright blue eyes.

“I will take good care of you, James Tiberius Kirk.” Defiance flashed in the eyes.

“I don’t need taking care of.” The augment shrugged.

“Then I shall do so anyway as you are my omega and I am your alpha. Such is the way of the world.” Kirk jumped up from the cot angrily.

“Until recently you were a terrorist; you killed Christopher Pike, you destroyed half of Starfleet, and you held Starfleet officers hostage. You can’t expect me to just roll over now because of your Biology bullshit!” Stifling a growl, Khan stood up and firmly gripped the shoulders of his recalcitrant omega.

“I have been giving you time to come to terms with your situation but I will not allow you to show me such disrespect. I am sorry for your loss however I am not capable of changing my previous actions. We are mates now and I will not settle for being treated as anything less.” The alpha watched as Kirk’s natural stubbornness warred with his new instincts to defer to his mate. Finally the gold clad shoulders slumped in submission. The superhuman was unhappy, however, to see a miserable look on the omega’s face and hints of tears in his eyes. He could see that Jim loathed his new instincts and was at a loss as to how to help a being adjust to them when he had his from birth.

He nuzzled the blond’s face. “Stay with me tonight,” he breathed, injecting a small amount of pleading into the request to give the starship captain some semblance of control. Jim glanced up uncertainly, his eyes shining, before giving a reluctant nod and reaching for his communicator.

“Spock, you have the con for the remainder of alpha shift.”

“Yes sir.”

**Notes for the Chapter:**

> I know that Chris Pine is actually slightly taller than Benedict but I decided that for whatever reason, Jim is slightly shorter than Khan in this. Maybe it's an alpha/omega thing?


	6. Chapter 6

**Summary for the Chapter:**

> Jim does some more adjusting to his circumstances and is insecure.

**Notes for the Chapter:**

> Hey guys,
> 
> Sorry for the super long wait, I moved back to the city where my university is and started school again. This update is a little bit shorter than previous ones but I decided I wanted to go ahead and get it out there for you.
> 
> Oh, and this chapter broke the 10,000 word mark which I'm really excited about since I don't think I've ever written anything that long before.

When Jim woke up, it was to a comforting warmth and even more comforting smell. He was slightly shocked to find himself tucked snugly into Khan’s chest but couldn’t find it within himself to move away. In fact, the captain found any resistance to his mate rapidly crumbling from a combination of fatigue and resignation. He still deeply missed Admiral Pike but he couldn’t deny that he had to make the best of the current situation and maybe that meant letting go of old grudges. He doubted Khan’s instincts would allow the former dictator to hurt Jim, and by extension, Jim’s friends, who had really become his family. 

The blond felt a pang as his thoughts once again turned to Khan’s family. If he told the man that his crew was alive, how would that change things? Would it be sufficient motivation for the superhuman to deny his instincts and leave Jim? As much as the niggling voice in his head told him that might be for the best, his chest ached at the prospect. He wondered how much of that came from being a pregnant omega but dismissed it as a pointless train of thought. Whatever the origins of his current feelings, they were his feelings now and he might as well start treating them as such.

Movement startled him out of his thoughts and he watched as the brunette slowly woke up, eyes blinking and a yawn on his lips. It struck him that this was a side he hadn’t really seen before, what with the heat and having to leave to go back to the bridge. For the few drowsy moments between asleep and awake, Khan exhibited a vulnerability that made him a little more human. The alpha’s eyes focused on blue and a pleased smile found its way onto his face at the realisation that his omega had not left. The Captain blushed and looked away, a little overwhelmed by the intense focus that was being directed at him. This caused Khan’s smile to widen as he lowered his head and nuzzled the blond. Before he knew it, Jim was nuzzling back and emitting a small keening sound. His eyes widened in shock at himself but then he relaxed, this was his life now and he better get used to it.

Pleased, Khan rewarded his newly cooperative omega with a heated kiss. He allowed a slight tussle for dominance but quickly took over the kiss, smiling into it when Kirk further relaxed his mouth and withdrew his tongue to let his alpha lead the way. His mate was learning things quickly. As he disconnected from the kiss, leaving a dazed Kirk, his hand lowered to lightly rub the Captain’s flat stomach. “It won’t be flat much longer,” he mused. Broken out of his daze, Jim glanced at his stomach with a frown. He still wasn’t down with the whole giving birth thing. Noticing the expression, Khan was quick to assure, “It seems strange to you now but your body is already adapting.” He lowered his head to place a kiss on his mate’s abdomen, “we are going to have a family.” Hearing the inflection on ‘family’, Jim gulped noisily.

“There’s uh...something I should tell you about...that.” The augment’s brow furrowed as he craned his head to look at Jim.

“Go on.” The deep voice intoned. The omega stepped away, wringing his hands and looking at anything but Khan.

“Yourcrewisn’tactuallydeadthey’restillfrozenintheircryotubesinsomewarehouseonearth.” For a moment, the captain was sure he would have to repeat that because there was no way anybody could have understood what he just said. He was reminded of the augments’ enhanced senses when Khan roared,

“My crew is not gone but hidden from me?!?” The blond flinched and braced himself for the coming blow. When it didn’t take place, he looked up to see his alpha looking at him with a sorrowful expression, although his hands still clenched and unclenched in anger.

“Jim....” He started, voice gentle, “...my mate...you must know that I would never intentionally strike you. However, I must know...how?” The omega let out a shaky breath before raising his eyes to rest on Khan’s nose.

“Spock didn’t lie; he said that he would send you your torpedoes and he did. What he didn’t mention was the fact that the cryotubes had all been removed and the torpedoes had been activated.” The augment nodded, remembering only too well the heart-shattering moment when he thought his family was gone forever. He cursed under his breath at underestimating the Vulcan’s sneakiness.

“Well, this certainly changes things.” He was torn from his burgeoning plans for releasing his comrades when he saw Jim’s face crumple in misery. Confused, he reached out only for the blond to turn away from him and step towards the glass. When Kirk spoke, his voice was strong and unbroken, reminding the alpha that this was a captain of a starship.

“I suppose this is goodbye, then.”

“Goodbye?” For once, Khan’s enhanced brain was at a total loss. The captain turned his head so that he could see the other man over his shoulder, although he kept his gaze lowered.

“As soon as I leave; you’ll escape, find a way back to earth, and wake up your crew. We’ll probably find ourselves on opposite sides again.” He placed a hand on his stomach subconsciously, “why would you need another family when you’ve already got one?” Before he could take another step towards the glass, a warmth was at his back and his alpha’s scent was wafting into his nostrils as arms encircled his waist. He couldn’t keep himself from leaning back imperceptibly. His head fell back automatically as the augment nuzzled into the crook where his neck met his shoulder.

“Although I admit I am sorely tempted to return to Earth and free my crew, I will not leave without my mate. Neither do I wish to upset you by forcibly separating you from your own crew.” This was rumbled against Jim’s skin. “No...I shall be patient.” Just as Jim was further relaxing into Khan’s embrace, his comm went off and Spock’s voice filled the cell, causing the augment to let out a growl of frustration.

“Captain, your presence is required on the bridge.” Sighing, the blond untangled himself from his mate and walked towards the edge of the cell.

“I guess I better see what’s going on. I do have a job to do on this ship.” He smirked slightly before placing his thumb on the glass and being let through. “I uh...guess I’ll see you later.” With that, he strode off, adjusting his command gold shirt as he went.


	7. Chapter 7

**Summary for the Chapter:**

> Some unexpected crazy shit happens.

**Notes for the Chapter:**

> I'm really sorry about the long wait but I promise I haven't abandoned it.

Upon reaching the bridge, Kirk was briefly surprised to see the face of Admiral Barnett before remembering the purpose of their current voyage. He smothered the encroaching feeling of dread as the admiral started talking.

“Captain Kirk, I understand that you have captured the criminal known as Khan and are bringing him to Earth.” It wasn’t a question. Shit.

“Yes sir, that is correct.”

“What is your ETA then, Captain?” Kirk glanced at Sulu.

“Lieutenant?”

“We are approximately 36 hours from touchdown, sir,” was the prompt reply.

“I will see you in 36 hours then Captain, Barnett out.” The screen flicked off.

 

Twenty minutes later and Jim was in the office of the CMO having a small panic attack while Bones nursed a glass of whiskey. He said that he was drinking for the both of them since the captain was now abstaining from alcohol but really, the blond knew that his friend was just being opportunistic.

“He did kill a lot of people, Jim. He has to answer for that...” Kirk sighed, knowing that his friend was right. “...however, he should get a trial and be able to state his case about what happened with Marcus. He wasn’t exactly unprovoked and he might get a lighter sentence because of that, provided he goes through some rehabilitation.” Jim perked up at that. Maybe there was a chance for them. Of course, Jim had no idea what he felt for Khan at the moment, but he wanted their baby to have both parents in his life.

Khan looked skeptical but was not going to say anything while his mate looked so hopeful. His plan was to escape the ship once they landed, wake his crew, and then come back for his omega, preferably with as few casualties as possible. The brunet sighed. Having James Kirk as a mate was clearly changing him. His second was probably going to hold it over him for years. Somehow though, as his omega snuggled into his arms and he could just smell a hint of his son’s scent, he couldn’t quite bring himself to care all that much.

 

Kirk was on the bridge when the first shot seemingly came out of nowhere and rocked the bridge. In the next second, the room was a flurry of activity, voices shouting and fingers flying over keyboards as the crew tried to figure out who was attacking them. Uhura turned around in her chair with her fingers on her earpiece.

“Captain, an unknown craft is hailing us.” Jim’s eyebrows furrowed.

“Put it up on the screen.” When the picture appeared, the inside of the ship’s bridge looked very similar to that of the Enterprise, suggesting that it was made by Starfleet. If it had been though, their sensors should have been able to pick up the model number. An unfamiliar face framed by short sandy hair was in the centre of the frame, looking fierce. As Jim’s eyes scanned the stranger, his eyes stopped on a familiar black uniform. It was familiar because the man currently sitting in the brig was wearing the same thing.

“Who are you and why have you fired on a Federation vessel?” Jim demanded. 

“We’re here to reclaim a member of our family that you currently have in your possession.”

“He is so because he has committed numerous crimes against Starfleet,” Spock spoke up. The man sneered.

“That’s what happens when you try to keep one of our kind on a leash. You humans fear us, yet you still try to force us to do your bidding.” Just as a cold feeling settled in Jim’s stomach, Spock’s eyebrow raised.

“Please elaborate.”

“A member of your precious Starfleet woke me up and demanded I continue the work that they forced our leader to start. Fortunately, it was very easy to lull them into a false sense of security, overpower them, wake the others and take a ship.”

“I am sorry that you went through that but I can assure you that the men who did that to you were not acting on Starfleet’s orders but   
rather, were following orders of a power-hungry man that is now dead.” Kirk explained calmly.

“And how am I to know that is the truth?”

“I can confirm it.” Shocked, Kirk turned to see his alpha walk onto the bridge. The security officers immediately moved to intercept but were motioned to stand down by the blond captain. Spock raised an eyebrow.

“Captain,” the man on screen saluted, clearly ruffled.

“Please tell me you didn’t break my ship.” Jim commented dryly. The augment appeared slightly flustered before drawing himself up and answering.

“I felt the need to ensure that you were unhurt.” Jim refused to allow the warm feeling to extend past the pit of his stomach. From her station, Uhura twisted her chair and looked wide-eyed at the captain. It seemed Spock hadn’t updated her on what had gone on. Kirk redirected his gaze to the screen to see the other augment, newly recollected, open his mouth.

“It is good to see you well, sir.” Khan nodded sharply.

“You as well, Derek. Is the entire crew with you?”

“Yes sir, all seventy two of us sir.” There were a few harsh intakes of breath from around the bridge. One augment had proven difficult enough for the federation to deal with; what damage could seventy three do? James stepped forward, attracting the man’s attention.

“We are transporting Khan to Earth where he will be given a chance to defend himself in a trial before the admirals. They will then determine what is to be the most appropriate sentence for his crimes against the federation. If your account is to be believed, you have committed actions that can be justified as self defence and the brass will have no reason not to let you go free.”

“And you believe that we will voluntarily leave one of our own at the mercy of your federation?” The man sneered. “One of the perpetrators of our torture may be gone but that in no way guarantees that there are no others.”

“While that is a logical conclusion to draw, I can assure you that the officials overseeing the trial are fair and will ensure that the process is not unduly influenced by any party,” Spock spoke up. Khan turned to the half-vulcan, even while his eyes were on Jim.

“I assure you, I will not be subjecting myself to any trial.” Taking his superior’s comment as a signal, the man on the screen speaks in murmurs to the crewmembers around him before ordering,

“Take down your shielding so that we may transport him to our ship.” There is a snort from Sulu but Jim calmly replies,

“I cannot do that.” He ignores the glare from his alpha, hot on his neck. He is a Starfleet captain and has a job to do. The expression on the face of the other augment darkens.

“Then you leave us no choice...” With that, the screen winks out. Understanding what was likely about to happen, Kirk tells the crew to prepare for combat.

“No!” The shout comes from their prisoner who is already moving towards Sulu’s station. When he is a few feet away however, Spock slams into his side and the two wrestle, each trying to overpower the other. Even with the subsequent addition of several security officers, Khan is not tiring. Already moving towards the scuffle, Jim is horrified to see the augment take a knife out of his boot and aim it at the half-vulcan.

“Khan! Stop!” Just as the alpha looked over, a shot rocked the bridge, sending the captain hard into the edge of a table. The force with which he hit it caused him to ricochet to the floor and hit his head. As he tried to push himself into a sitting position, he dazedly wondered where all the blood on the floor was coming from, he hadn’t hit his head that hard. Three more shots hit the ship in quick succession and the blond heard Sulu yell out that the shields were down but Scotty was already working on it. Jim smiles wryly even as gentle hands push him to lie down; good ol’ Scotty. A burst of blue light is seen out of the corner of his eye and there is a commotion. From over the chaos, the downed captain can just make out Spock calmly ordering the shields to be put back up as soon as possible and for them to warp away. He vaguely hears Uhura’s voice telling him to stay with them before his vision fades to black.

 

On the other ship, Khan has barely materialised in the transporter room before he is stepping off the platform and telling the officer behind the controls to lock onto another figure, that of the captain. The young woman’s fingers fly along the keys for a few moments before she looks up at her captain,

“I’m sorry sir, but the shields are back up and I can no longer lock on to anybody.” The brunet swears before running towards the bridge where he is greeted by his first officer.

“What is the status of the Enteprise?” He asks, brushing aside the greetings.

“They warped away sir, I suppose they wanted to lick their wounds in private.” The man informed him smugly. Khan let out a roar of rage and slammed his fist down on the nearest table, severely denting it. While his crew did not show any signs of fear, they were clearly startled and confused by their leader’s reaction.

“We have to follow them.”

“I’m sorry sir, but as they are most likely headed back to Earth, I must insist that it would not be a good idea. While one ship is no match for us, an entire fleet will be much more formidable.” Khan growled but nodded, acknowledging his first officer’s good judgement. He resolved to take the time to formulate a plan to get his omega back; only then would his family be complete.


	8. Chapter 8

**Notes for the Chapter:**

> Hey look! It's only been three months since the last update; I'm getting better at this!
> 
> I know, I know *hangs head*
> 
> I'm going to try really hard to put out the next chapter in less time than that.

“Get out of the way!” was the only warning crewmembers got before Dr Mccoy barrelled down the hallway with an antiquated rolling stretcher that held the captain. The first officer was keeping pace with it, eyes flicking along the prone body, trying to pinpoint where all the blood was coming from. Leonard had a nasty suspicion he knew what was happening but hoped that he was wrong.

As they careened into the medbay, Bones started barking orders at the nurses as Spock gently lifted his friend onto a biobed. A nurse started taking scans while the gruff doctor used some surgical scissors to cut off the blond’s clothing. The blood concentrated around the seat and rear of the pants, confirming Leonard’s grim thoughts. Once the fabric was removed, a wave of blood that had previously been held back spilled out, some even splashing onto the floor as a result of the forceful exit. Spock stepped back, looking vaguely perturbed.

“I am unfamiliar with the Captain’s current biology, Doctor. Are you aware of what is causing his blood loss?” The gruff man looked sadly at his prone friend before answering.

“Jim is undergoing a miscarriage.” A brief look of sorrow flashed through the half-vulcan’s eyes, his only visible reaction to the news.

 

Jim Kirk woke to the cacophony of whirrs and beeps that he was really getting tired of waking up to. He was trying to push himself into a sitting position just as his surly CMO walked through the door. Once again, he wondered if it was coincidence or if the man had some kind of freaky sixth sense that told him exactly when his patients were waking. “You lie your ass back down Kirk or so help me...” Jim rolled his eyes and kept going until a sharp pain shot through his side. He landed on his back, gasping in pain. “I told you,” came the gruff reprimand as a hand gently moved him back into the right position.

“What the hell happened?” Jim was surprised to see his friend’s eyes go a bit grim. 

After a few moments of clear deliberation, Leonard opened his mouth and stated softly, “You’ve undergone a miscarriage, Jim.”   
The captain felt his heart drop as he stared wide-eyed at Bones. His gaze dropped unseeingly to his right hand, which fisted and relaxed on his lap. The brunette continued, “Normally, I would give my patients some time to adjust but somehow I don’t think you’re the type.” The blond scrunched his eyes shut to beat back the tears before opening them again and nodding. He could get through this. He was a captain; he had to get through this. He had always known that a child was never really in the cards for him anyway...but god he had wanted him so badly. 

Once he was sure he could speak without his voice shaking he asked, “And what of the prisoner?” Not Khan...never Khan; he doesn’t know why he ever let himself believe in the silly fairytale notion of being a happy family. McCoy shrugged.

“Gone. Scotty’s trying to find a trace to the source of the transport signal but he doesn’t have high hopes.”   
Kirk nodded curtly, “Let me know if anything has changed.” 

The doctor’s eyes narrowed, “you need to rest for at least 36 hours, kid; if I need to keep you here for that to happen, I’ll do it.” Jim rolled his eyes, knowing that it would rile up his friend. The older man was opening his mouth to let loose what would most likely be a string of colourful language when there was a knock on the door. Grumbling, Bones walked over to the entrance and opened the door.  
He held it open as Uhura glided in, muttered that ‘she could have a turn with the dumb kid’, and left. The communications officer glanced bemusedly at the blue retreating back before turning her attention to the captain. Her face was perfectly composed but for the slightly furrowed brow that denoted her concern. She pulled over a seat and gracefully sat down. 

“Spock told me what happened. How are you doing?” she asked softly. Jim searched her eyes and was relieved to find no trace of pity in them, only sympathy. He shrugged and gave a cocky half-smile.

“A little banged up but Bones says a little rest and I’ll be good as new.” Nyota smiled and let out a huff.

“While I’m sure that’s a gross understatement, I trust Leonard to wrangle you back into bed if he deems it necessary.”

“Hey! As the Captain I’m the wrangler, not the wrangl-ee.” This turned the smile into a full blown laugh.

Slowly, Kirk worked himself into a reclined position, his appreciation for Uhura rising when she didn’t rush to help him. “How is my ship?” Nyota’s back straightened as the atmosphere became more professional.

“Scotty’s got everything up and running at optimal capacity. He says that there are some minor structural issues that he wants to get checked out once we dock.” The Captain winced at the reminder that they were expected to deliver a prisoner to Starfleet.

“When will we be arriving, Lieutenant?”

“We are expecting to dock in 03:00 hours.” The blond dropped his head back onto the pillow and clenched his eyes shut. Uhura reached forward and placed a well-manicured hand gently on Jim’s knee. “I’m sure the admiralty will understand. There was no way we could have defended ourselves against that kind of firepower. Some of the crew’s still pretty shaken up over how they came out of nowhere.”  
Kirk was starting to lift his hand up to his face when there was a cautionary twinge in his ribs so he settled for a strained smile. “I can handle the admirality.” The communications officer looked like she was about to say something but decided against it and patted his knee while standing up.

“You focus on getting some rest, Spock has everything under control,” she said kindly.

“Oh, I’m sure he has,” was said with fond exasperation. They shared a grin before Nyota walked out. Jim felt warmth in his chest at the knowledge that all his friends cared so much about his well-being; for all that they had completely different ways of showing it. Speaking of which, Bones soon swept into the room with a nurse in tow. “We’re going to check you over once more before you go back to sleep” was the only explanation given before the Captain found himself being poked and prodded by two sets of uncomfortably cold hands. He gave a few token grumbles but was quickly realizing how tired he was as he struggled to keep his eyes open. Hands eased him down so he was lying on his back again and he thought he told Bones to wake him in three hours but he wasn't sure.

**Notes for the Chapter:**

> So, I hope that the part with Uhura wasn't too weird. She hadn't appeared much in the fic and I wanted to establish a friendship between her and Jim to go with the friendship between Jim and Spock. When they're not being my OT3, they're my BrOT3


End file.
